This dataset contains assembled sequence contigs, input and results files of phylogenetic analyses, input matrices for haplotype reconstructions, and input and results files for ancestral range reconstructions from the article "Evolution of Crematogaster sordidula (Hymenoptera, Formicidae) ants in the Mediterranean region during Plio-Pleistocene climatic changes." by Voges et al. (2026). The dataset is organized as follows: 1_Assembled_contigs_from_Voges_et_al_2026_Phylogeny_Crematogaster_sordidula.zip Folder containing spades assemblies (version SPADES v3.15.4) for all 126 taxa analyzed in the study. 2_Phylogenetic_input_and_result_files_from_Voges_et_al_2026_Phylogeny_Crematogaster_sordidula.zip 2.1_MLIQTREE: Ten subfolders contain files for each maximum likelihood (ML) analysis performed with IQ-TREE v.1.6.8. Analyses are labeled using the same terminology as in Voges et al. Additionally one folder with configuration files used in the Phyluce Pipeline. 2.1.1_Config_files: Configuration files used as input in the Phyluce Pipeline at different steps. Furthermore, it contains a folder including .config files used as input for PartionFinder2 (v.2.1.1) and .log files for each partition scheme. 2.1.2_80%-untrimmed: The directory contains the .nex input file, as well as the .charsets, .phylip, .contree, .iqtree , .log, .treefile output files from the ML analysis using the partitioned 80% untrimmed matrix in IQTREE (v1.6.8). 2.1.3_80%-0.95-spruceup: SWSC-partitioned analysis performed on the 80% taxon-complete nucleotide matrix with a distance cut-off value of 0.95 in Spruceup v2020.2.19. Included are .phy and .nex input files, and .contree, .iqtree, .log, .treefile output files for this partitioned ML analysis performed in IQ-TREE (v1.6.8). 2.1.4_80%-0.97-spruceup: SWSC-partitioned analysis performed on the 80% taxon-complete nucleotide matrix with a distance cut-off value of 0.97 in Spruceup v2020.2.19. Included are .phy and .nex input files, and .contree, .iqtree, .log, .treefile output files for this partitioned ML analysis performed in IQ-TREE (v1.6.8). 2.1.5_80%-0.98-spruceup: SWSC-partitioned analysis performed on the 80% taxon-complete nucleotide matrix with a distance cut-off value of 0.98 in Spruceup v2020.2.19. Included are .phy and .nex input files, and .contree, .iqtree, .log, .treefile output files for this partitioned ML analysis performed in IQ-TREE (v1.6.8). 2.1.6_90%-untrimmed: The directory contains the .nex input file, as well as the .charsets, .phylip, .contree, .iqtree , .log, .treefile output files from the ML analysis using the partitioned 90% untrimmed matrix in IQTREE (v1.6.8). 2.1.7_90%-0.95-spruceup: SWSC-partitioned analysis performed on the 90% taxon-complete nucleotide matrix with a distance cut-off value of 0.95 in Spruceup v2020.2.19. Included are .phy and .nex input files, and .contree, .iqtree, .log, .treefile output files for this partitioned ML analysis performed in IQ-TREE (v1.6.8). 2.1.8_90%-0.97-spruceup: SWSC-partitioned analysis performed on the 90% taxon-complete nucleotide matrix with a distance cut-off value of 0.97 in Spruceup v2020.2.19. Included are .phy and .nex input files, and .contree, .iqtree, .log, .treefile output files for this partitioned ML analysis performed in IQ-TREE (v1.6.8). 2.1.9_90%-0.98-spruceup: SWSC-partitioned analysis performed on the 90% taxon-complete nucleotide matrix with a distance cut-off value of 0.98 in Spruceup v2020.2.19. Included are .phy and .nex input files, and .contree, .iqtree, .log, .treefile output files for this partitioned ML analysis performed in IQ-TREE (v1.6.8). 2.1.10_SNP-14R: Two subfolder contain files for each maximum likelihood (ML) analysis performed with IQ-TREE v.1.6.8. 2.1.10.a_SNPcompleteTree: The directory contains the .nex input file, as well as the .charsets, .phylip, .contree, .iqtree , .log, .treefile output files from the ML analysis using the partitioned 90% complete SNP matrix in IQTREE (v1.6.8). 2.1.10.b_SNPreducedTree14R: The directory contains the .phylip input file, as well as the .charsets, .phylip, .contree, .iqtree , .log, .treefile output files from the ML analysis using the partitioned 90% reduced SNP matrix including each two taxa per 14 Regions, in IQTREE (v1.6.8). 2.2_ASTRAL: The folder contains the .treefile and .iqtree file from the first step ML IQTREE analysis together with the resulting .nwk file used as input for coalescent species tree analysis in ASTRAL-III v.5.7.8, as well as .los, .tre, .nex, .iqtree, .treefile output files. 2.3_Dating: Contains two subfolders with the input and output files from the two-step dating analysis. 2.3.1_MCMCTREE contains alignments (.phy), configuration files (.ctl) and input tree file (input.tre), as well as the resulting chronogram tree file (.tre) from each analysis performed with MCMCTREE in PAML4.10.6, as outlined in Voges et al. 2.3.2_SNAPP contains a subfolder (2.3.2a) with additional scripts used for the dating analysis in SNAPP version 1.6.1 in BEAST version 2.7, as well as the .xml and .nexus input files for SNAPP and the .trees output file. 2.4_COIAnalysis: Contains three subfolders with files for the maximum likelihood (ML) analysis performed with IQ-TREE v.1.6.8. 2.4.2_Barcodes contains the .fasta files for the COI Barcode data obtained from the UCE bycatch for each sample. 2.4.3_400bpCOI contains the .fasta input file used for the alignment in MAFFT v.752, the resulting .nex file used as input for IQTREE (v1.6.8), as well as the .contree, .iqtree, .log, .treefile ouput files. 3_Ancestral_reconstruction_from_Voges_et_al_2026_Phylogeny_Crematogaster_sordidula: Two subfolders containing all input and output files from the ancestral area reconstruction in BioGeoBEARS in R (v.4.3.0) 3.1_InputDataR: Contains the .nexus input tree, the .csv input trait matrix and the .R code used in BioGeoBEARS in R (v.4.3.0) for the ancestral area reconstruction. 3.2_OutputDataR: The Rproject file (.RData) contains the results for the ancestral reconstruction analyses as described in the paper, and additionally, .txt files with comparisons and results from the different models. 4_Haplotype_reconstructions_from_Voges_et_al_2026_Phylogeny_Crematogaster_sordidula.zip: contains the .nex input trait matrices used for the haplotype reconstructions in PopART 5_Metadata_population_genomic_analyses_from_Voges_et_al_2026_Phylogeny_Crematogaster_sordidula.zip: contains the .fasta SNP alignment, the .new tree topology inferred from the UCE dataset, the .vcf dataset containing all SNPs, the .py python script used to filter one SNP per UCE locus, the .vcf file containing one SNP per locus, a .txt file to remove the outgroup samples from the SNP dataset, .csv tables containing population and region information per sample (see also Table S4). 6_PLINK_files_from_Voges_et_al_2026_Phylogeny_Crematogaster_sordidula.zip: contains the .bed, .bim, .fam, .nosex and .log outputfiles from the PLINK analysis. 7_Principal_component_analysis_from_Voges_et_al_2026_Phylogeny_Crematogaster_sordidula.zip: contains the .eigenval, .eigenvec and .nosex results from the PCA analysis 8_ADMIXTURE_analysis_from_Voges_et_al_2026_Phylogeny_Crematogaster_sordidula.zip: contains four subfolders with results from the admixture analysis used as input for population genomic reconstructions in R (v.4.5.1). 8.1_CV_errors: contains results of the 10-fold cross-validation for K = 1–10. 8.2_P_matrices: contains .P files for all K 8.3_Q_matrices: contains .Q files for all K 8.4_logs: contains .log files for each K and admixture run. 9_Pairwise_genetic_differentiation_between_regions_from_Voges_et_al_2026_Phylogeny_Crematogaster_sordidula.zipcontains .fst and .nosex files from the Fst analysis calculated in PLINK. 10_R_scripts_for_population_genomics_from_Voges_et_al_2026_Phylogeny_Crematogaster_sordidula.zip: contains three R scripts written to calculate, analyze admixture, PCA, genetic connectivity and pairwise Fst in. this study.